Michigan COVID Data

Get link for data:

from urllib.request import urlopen

from bs4 import BeautifulSoup

# Get data into pandas df
URL = "https://www.michigan.gov/coronavirus/0,9753,7-406-98163_98173---,00.html"
HTML = urlopen(URL).read().decode("utf-8")
start_index = HTML.find("shortdesc")
end_index = HTML.find("footerArea")
data = HTML[start_index:end_index]
soup = BeautifulSoup(data, features="html.parser")
links = [link.get('href') for link in soup.find_all('a')]
finallink = "https://michigan.gov" + \
    [i for i in links if "by_Date" in i][0]

Download data:

temp <- tempfile()
download.file(py$finallink, destfile = temp)
mi_data <- readxl::read_excel(temp)

Clean data:

mi_data = r.mi_data
max_date = max(mi_data["Updated"])
agg_data = mi_data.groupby(["Date"], as_index=False).sum()

date_update = format(py$max_date, '%d %b %Y')
mi_cases_by_day = py$agg_data
head(mi_cases_by_day)

##                  Date Cases Deaths Cases.Cumulative Deaths.Cumulative
## 1 2020-02-29 19:00:00    14      0               14                 0
## 2 2020-03-01 19:00:00    13      1               27                 1
## 3 2020-03-02 19:00:00    22      0               49                 1
## 4 2020-03-03 19:00:00    24      0               73                 1
## 5 2020-03-04 19:00:00    26      0               99                 1
## 6 2020-03-05 19:00:00    42      0              141                 1

Initial Data Visualization:

plot_ly(
  mi_cases_by_day,
  x = ~Date,
  y = ~Cases
)

With 7 day moving average and deaths:

mi_cases_by_day <- mi_cases_by_day %>%
  mutate(
    cases_ma = rollapply(Cases, 7, mean, align = "center", fill = 0),
    deaths_ma = rollapply(Deaths, 7, mean, align = "center", fill = 0)
  )

ay <- list(tickfont = list(color = "red"),
  overlaying = "y",
  side = "right",
  title = "Deaths")

plot_ly(mi_cases_by_day,x = ~Date) %>% 
  # Cases
  add_trace(y = ~Cases, alpha = .6, name = "Cases", type = "scatter", 
            mode = 'markers') %>%
  # Cases MA
  add_lines(y = ~cases_ma, alpha = .8, name = "Cases MA", mode = 'markers') %>%
  # Deaths
  add_trace(name = "Deaths", yaxis = "y2", alpha = .15, y = ~Deaths, x = ~Date,
            color = I("red"), type = "scatter", mode = 'markers') %>%
  # Deaths MA
  add_lines(name = "Deaths MA", yaxis = "y2", y = ~deaths_ma, x = ~Date,
            line = list(color = I("red")), alpha = .8/4, mode = 'markers') %>%
  layout(
    title = "Michigan COVID Cases/Deaths<br>With 7-day Moving Average",
    yaxis2 = ay, legend = list(x = 0.6, y = 0.9),margin = list(r = 50, t = 50)
  )